Added calc_genoprob_fst() which combines calc_genoprob() and fst_genoprob() to save use of RAM when calculating genotype probabilties.
Added genoprob_to_alleleprob_fst() which combines genoprob_to_alleleprob() and fst_genoprob() to save use of RAM when converting genotype probabilties to allele dosages.
Added summary() and print() functions for "fst_genoprob" objects.
Rewrote the vignette using the iron dataset, so that it’s faster to build.
class(), avoiding constructions like "blah" %in% class(object) and instead using inherits(object, "blah").Renumbering to match R/qtl2 version
Use Markdown for function documentation, throughout
fst_genoprob(): added quiet argument, to replace verbose which we’ll ultimately remove. Also added an argument overwrite; if FALSE (the default), refuse to overwrite the .fst files.
Renamed fst2calc_genoprob() as fst_extract(). The function with the original name will remain for a while, but will give a warning.
Renamed fst_genoprob_restore() as `fst_restore(). The function with the original name will remain for a while, but will give a warning.
When fst_genoprob() creates the set of .fst files with the genotype probabilities, it also creates a .rds file with the index object. Load this object with readRDS(). cbind.fst_genoprob() and rbind.fst_genoprob() will write the index .fst file for the new object.
Added overwrite and quiet arguments to cbind.fst_genoprob() and rbind.fst_genoprob().
Added a function fst_path() for viewing the path to the files behind an "fst_genoprob" database.
Added a function fst_files() for viewing the set of files behind an "fst_genoprob" database.
Added a function replace_path() for replacing the file path within a "fst_genoprob" object.